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Yorodumi- PDB-1ook: Crystal Structure of the Complex of Platelet Receptor GPIb-alpha ... -
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-Basic information
Entry | Database: PDB / ID: 1ook | |||||||||
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Title | Crystal Structure of the Complex of Platelet Receptor GPIb-alpha and Human alpha-Thrombin | |||||||||
Components |
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Keywords | HYDROLASE / Leucine rich repeats | |||||||||
Function / homology | Function and homology information thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / ligand-gated ion channel signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / release of sequestered calcium ion into cytosol / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / extracellular matrix / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell morphogenesis / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / cell adhesion / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / external side of plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Varughese, K.I. / Celikel, R. / Ruggeri, Z.M. | |||||||||
Citation | Journal: Science / Year: 2003 Title: Modulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha Authors: Celikel, R. / McClintock, R.A. / Roberts, J.R. / Mendolicchio, G.L. / Ware, J. / Varughese, K.I. / Ruggeri, Z.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ook.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ook.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ook.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/1ook ftp://data.pdbj.org/pub/pdb/validation_reports/oo/1ook | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein/peptide , 2 types, 2 molecules AP
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: THROMBIN A CHAIN / Source method: isolated from a natural source / Details: Purified from plasma / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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#3: Protein/peptide | Mass: 419.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized |
-Protein , 2 types, 2 molecules BG
#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: THROMBIN B CHAIN / Source method: isolated from a natural source / Details: Purified from plasma / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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#4: Protein | Mass: 32466.920 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Mutation: C65A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GP1BA / Production host: Escherichia coli (E. coli) / References: UniProt: P07359 |
-Sugars , 2 types, 2 molecules
#5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#7: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 393 molecules
#6: Chemical | ChemComp-CL / |
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#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 52.81 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 6000, Ammonium Phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.033167 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2002 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033167 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 35360 / Num. obs: 35360 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.2 % / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.066 / Net I/σ(I): 38.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 5.2 / Rsym value: 0.292 / % possible all: 97.5 |
Reflection | *PLUS Num. measured all: 608108 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 97.5 % / Rmerge(I) obs: 0.292 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.24 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 15 Å / Num. reflection obs: 32958 / Num. reflection Rfree: 1722 / Rfactor Rfree: 0.26 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.345 / Rfactor Rwork: 0.2831 |